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Title: | Nuclear RNA sequencing of the mouse erythroid cell transcriptome |
Authors: | Mitchell, JA Clay, I Umlauf, D Chen, CY Moir, CA Eskiw, CH Schoenfelder, S Chakalova, L Nagano, T Fraser, P |
Issue Date: | 2012 |
Publisher: | Public Library of Science |
Citation: | PLoS One, 7(11): e49274, Nov 2012 |
Abstract: | In addition to protein coding genes a substantial proportion of mammalian genomes are transcribed. However, most transcriptome studies investigate steady-state mRNA levels, ignoring a considerable fraction of the transcribed genome. In addition, steady-state mRNA levels are influenced by both transcriptional and posttranscriptional mechanisms, and thus do not provide a clear picture of transcriptional output. Here, using deep sequencing of nuclear RNAs (nucRNA-Seq) in parallel with chromatin immunoprecipitation sequencing (ChIP-Seq) of active RNA polymerase II, we compared the nuclear transcriptome of mouse anemic spleen erythroid cells with polymerase occupancy on a genome-wide scale. We demonstrate that unspliced transcripts quantified by nucRNA-seq correlate with primary transcript frequencies measured by RNA FISH, but differ from steady-state mRNA levels measured by poly(A)-enriched RNA-seq. Highly expressed protein coding genes showed good correlation between RNAPII occupancy and transcriptional output; however, genome-wide we observed a poor correlation between transcriptional output and RNAPII association. This poor correlation is due to intergenic regions associated with RNAPII which correspond with transcription factor bound regulatory regions and a group of stable, nuclear-retained long non-coding transcripts. In conclusion, sequencing the nuclear transcriptome provides an opportunity to investigate the transcriptional landscape in a given cell type through quantification of unspliced primary transcripts and the identification of nuclear-retained long non-coding RNAs. |
Description: | Copyright @ 2012 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
URI: | http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0049274 http://bura.brunel.ac.uk/handle/2438/7046 |
DOI: | http://dx.doi.org/10.1371/journal.pone.0049274 |
ISSN: | 1932-6203 |
Appears in Collections: | Biological Sciences Publications Dept of Life Sciences Research Papers |
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